The LIHC RPPA data submitted by MDACC were discovered to be mislabelled MESO samples. The analyses and standard data pipelines for LIHC have been re-run using the corrected samples submitted in March, and the nozzle reports now contain notices of the discrepancies.
The following table shows the changes in sample counts for RPPA data as a result of this patch:
All mRNASeqV2 packages and derived packages have been updated for MESO and SKCM. Please ensure you are using the following 1.0 archives rather than the 0.0 ones for these cohorts:
This is due to multiple versions of the same protocol in the SDRFs for these cohorts causing our data ingestor to drop samples. After conferring with the submitters, we've updated our tools to make an exception for this with RNASeqV2 data, and added the dropped samples back to the run.
Due to a PHI breach at one of our upstream data sources, where protected health information was accidentally included in the clinical data files for the Adrenocortical Carcinoma disease study (ACC), we have deleted all of the ACC stddata archives for the following tasks
from the December 2013 and January 2014 stddata runs (2013_12_10 and 2014_01_15, respectively). These clinical data archives will re-appear in the forthcoming February 2014 stddata run. No downstream Firehose analyses were impacted by this PHI breach.
Due to a dicing issue, the PAAD MAF was processed rather than the LGG one for the 12/21 run. The correct file had been swapped in prior to the run, but the dicer did not recognize the swap, and didn't process the LGG MAF. Our next run will have the correct LGG MAF. This affects mutation results for LGG in the analyses__2012_12_21 run as well.
Our internal rewiring to accommodate normal samples induced a hiccup which required several MAF packager files to be reissued for the stddata__2012_10_24 run. The new files have been uploaded to the DCC and will be available in the protected data tree pending internal mirroring by the DCC, or may be downloaded presently via firehose_get. The newly issued files are identifiable as
The LUAD mafs we ingested in stddata__2012_08_25 had non-standard headers. We've since enhanced our MAF ingestor to correct such headers when detected, and re-released the LUAD maf yesterday (17 Sept. 2012). New tarballs are available from firehose_get, and soon the DCC, as: